1
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Su Z, Chen A, Lipkowski J. Electrochemical and Infrared Studies of a Model Bilayer of the Outer Membrane of Gram-Negative Bacteria and its Interaction with polymyxin─the Last-Resort Antibiotic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8248-8259. [PMID: 38578277 DOI: 10.1021/acs.langmuir.4c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
A model bilayer of the outer membrane (OM) of Gram-negative bacteria, composed of lipid A and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE), was assembled on the β-Tg modified gold (111) single crystal surface using a combination of Langmuir-Blodgett and Langmuir-Schaefer transfer. Electrochemical and spectroscopic methods were employed to study the properties of the model bilayer and its interaction with polymyxin. The model bilayer is stable on the gold surface in the transmembrane potential region between 0.0 and -0.7 V. The presence of Mg2+ coordinates with the phosphate and carboxylate groups in the leaflet of lipid A and stabilizes the structure of the model bilayer. Polymyxin causes the model bilayer leakage and damage in the transmembrane potential region between 0.2 and -0.4 V. At transmembrane potentials lower than -0.5 V, polymyxin does not affect the membrane integrity. Polymyxin binds to the phosphate and carboxylate groups in lipid A molecules and causes the increase of the tilt angle of acyl chains and the decrease of the tilt of the C═O bond. The results in this paper indicate that the antimicrobial activity of polymyxin depends on the transmembrane potential at the model bilayer and provides useful information for the development of new antibiotics.
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Affiliation(s)
- ZhangFei Su
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Aicheng Chen
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jacek Lipkowski
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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2
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Pengelly RJ, Bakhtiar D, Borovská I, Královičová J, Vořechovský I. Exonic splicing code and protein binding sites for calcium. Nucleic Acids Res 2022; 50:5493-5512. [PMID: 35474482 PMCID: PMC9177970 DOI: 10.1093/nar/gkac270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/12/2022] Open
Abstract
Auxilliary splicing sequences in exons, known as enhancers (ESEs) and silencers (ESSs), have been subject to strong selection pressures at the RNA and protein level. The protein component of this splicing code is substantial, recently estimated at ∼50% of the total information within ESEs, but remains poorly understood. The ESE/ESS profiles were previously associated with the Irving-Williams (I-W) stability series for divalent metals, suggesting that the ESE/ESS evolution was shaped by metal binding sites. Here, we have examined splicing activities of exonic sequences that encode protein binding sites for Ca2+, a weak binder in the I-W affinity order. We found that predicted exon inclusion levels for the EF-hand motifs and for Ca2+-binding residues in nonEF-hand proteins were higher than for average exons. For canonical EF-hands, the increase was centred on the EF-hand chelation loop and, in particular, on Ca2+-coordinating residues, with a 1>12>3∼5>9 hierarchy in the 12-codon loop consensus and usage bias at codons 1 and 12. The same hierarchy but a lower increase was observed for noncanonical EF-hands, except for S100 proteins. EF-hand loops preferentially accumulated exon splits in two clusters, one located in their N-terminal halves and the other around codon 12. Using splicing assays and published crosslinking and immunoprecipitation data, we identify candidate trans-acting factors that preferentially bind conserved GA-rich motifs encoding negatively charged amino acids in the loops. Together, these data provide evidence for the high capacity of codons for Ca2+-coordinating residues to be retained in mature transcripts, facilitating their exon-level expansion during eukaryotic evolution.
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Affiliation(s)
- Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Ivana Borovská
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Jana Královičová
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
- Slovak Academy of Sciences, Institute of Zoology, 845 06 Bratislava, Slovak Republic
| | - Igor Vořechovský
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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3
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Khairalla B, Brand I. Membrane Potentials Trigger Molecular-Scale Rearrangements in the Outer Membrane of Gram-Negative Bacteria. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:446-457. [PMID: 34963050 DOI: 10.1021/acs.langmuir.1c02820] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The structural complexity of the cell envelope of Gram-negative bacteria limits the fabrication of realistic models of bacterial cell membranes. A vertical Langmuir-Blodgett withdrawing was used to deposit a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) monolayer on the Au(111) surface. The second leaflet composed of di[3-deoxy-D-manno-octulosonyl]-lipid A (KLA) was deposited using Langmuir-Schaefer transfer. The use of an electrode material as a support for the POPE-KLA bilayer allowed electrochemical control of the membrane's stability, compactness, and structure. Capacitance-potential curves showed a typical pattern for the supported lipid bilayers electrochemical characteristic. The minimum membrane capacitance was ∼4 μF cm-2 and did not change in the following desorption-adsorption cycles, indicating the presence of a stable bilayer structure with an asymmetric composition of both leaflets. However, at a molecular scale, as elucidated in spectroelectrochemical experiments, large differences in the response of both leaflets to electric potentials were observed. The acyl chains in POPE and KLA existed in a liquid state. The quantitative analysis of the CH stretching modes indicated potential-driven reorientations in the hydrophobic fragment of the bilayer, already in the adsorbed state. To assign observed rearrangements to POPE and KLA lipids in both leaflets, per-deuterated d31-POPE was transferred into the inner leaflet. Since no potential-dependent changes of the CD2 stretching modes in the d31-POPE-KLA bilayer were observed, reorientations in the acyl chain region were assigned to the KLA molecules. Mg2+ ions were bound to the polar head groups of KLA. The strength of electrostatic interactions in the polar head group region of KLA was dependent on the direction of the electric field. At negative electric potentials, the binding of divalent cations weakened, which gave the KLA molecules increased orientational flexibility. This behavior in electric fields is peculiar for the outer membrane and indicates that the microbial cell membranes have different electrochemical properties than phospholipid bilayers.
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Affiliation(s)
- Bishoy Khairalla
- Department of Chemistry, University of Oldenburg, 26111 Oldenburg, Germany
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg, 26111 Oldenburg, Germany
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4
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Tsvetkov PO, Roman AY, Baksheeva VE, Nazipova AA, Shevelyova MP, Vladimirov VI, Buyanova MF, Zinchenko DV, Zamyatnin AA, Devred F, Golovin AV, Permyakov SE, Zernii EY. Functional Status of Neuronal Calcium Sensor-1 Is Modulated by Zinc Binding. Front Mol Neurosci 2018; 11:459. [PMID: 30618610 PMCID: PMC6302015 DOI: 10.3389/fnmol.2018.00459] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/28/2018] [Indexed: 11/29/2022] Open
Abstract
Neuronal calcium sensor-1 (NCS-1) protein is abundantly expressed in the central nervous system and retinal neurons, where it regulates many vital processes such as synaptic transmission. It coordinates three calcium ions by EF-hands 2-4, thereby transducing Ca2+ signals to a wide range of protein targets, including G protein-coupled receptors and their kinases. Here, we demonstrate that NCS-1 also has Zn2+-binding sites, which affect its structural and functional properties upon filling. Fluorescence and circular dichroism experiments reveal the impact of Zn2+ binding on NCS-1 secondary and tertiary structure. According to atomic absorption spectroscopy and isothermal titration calorimetry studies, apo-NCS-1 has two high-affinity (4 × 106 M-1) and one low-affinity (2 × 105 M-1) Zn2+-binding sites, whereas Mg2+-loaded and Ca2+-loaded forms (which dominate under physiological conditions) bind two zinc ions with submicromolar affinity. Metal competition analysis and circular dichroism studies suggest that Zn2+-binding sites of apo- and Mg2+-loaded NCS-1 overlap with functional EF-hands of the protein. Consistently, high Zn2+ concentrations displace Mg2+ from the EF-hands and decrease the stoichiometry of Ca2+ binding. Meanwhile, one of the EF-hands of Zn2+-saturated NCS-1 exhibits a 14-fold higher calcium affinity, which increases the overall calcium sensitivity of the protein. Based on QM/MM molecular dynamics simulations, Zn2+ binding to Ca2+-loaded NCS-1 could occur at EF-hands 2 and 4. The high-affinity zinc binding increases the thermal stability of Ca2+-free NCS-1 and favours the interaction of its Ca2+-loaded form with target proteins, such as dopamine receptor D2R and GRK1. In contrast, low-affinity zinc binding promotes NCS-1 aggregation accompanied by the formation of twisted rope-like structures. Altogether, our findings suggest a complex interplay between magnesium, calcium and zinc binding to NCS-1, leading to the appearance of multiple conformations of the protein, in turn modulating its functional status.
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Affiliation(s)
- Philipp O Tsvetkov
- Aix-Marseille University, CNRS, INP, Institute of Neurophysiopathology, Faculty of Pharmacy, Marseille, France
| | - Andrei Yu Roman
- Institute of Physiologically Active Compounds (RAS), Chernogolovka, Russia
| | - Viktoriia E Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aliya A Nazipova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Marina P Shevelyova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Vasiliy I Vladimirov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - Michelle F Buyanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - Andrey A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - François Devred
- Aix-Marseille University, CNRS, INP, Institute of Neurophysiopathology, Faculty of Pharmacy, Marseille, France
| | - Andrey V Golovin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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5
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Brand I, Matyszewska D, Koch KW. Binding of a Myristoylated Protein to the Lipid Membrane Influenced by Interactions with the Polar Head Group Region. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14022-14032. [PMID: 30360613 DOI: 10.1021/acs.langmuir.8b02265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many cytoplasmic proteins contain a hydrophobic acyl chain, which facilitates protein binding to cell membranes. Hydrophobic interactions between the exposed acyl chain of the protein and hydrocarbon chains of lipids in the cell membrane are the driving force for this specific lipid-protein interaction. Recent studies point out that in addition to hydrophobic interactions the charge-charge and charge-dipole interactions between the polar head groups and basic amino acids contribute significantly to the binding process. Recoverin possesses a myristoyl chain at the N-terminus. In the presence of Ca2+ ions, the protein undergoes structural rearrangements, leading to the extrusion of the myristoyl chain, facilitating the protein binding to the membrane. In this work, we investigate the impact of interactions between the polar head group region of lipid molecules and recoverin which binds to the model membrane. The interaction with a planar lipid bilayer composed of phosphatidylcholine and cholesterol with myristoylated and nonmyristoylated recoverin is studied by in situ polarization modulation infrared reflection absorption spectroscopy. The binding of recoverin to the lipid bilayer depends on the transmembrane potential, indicating that the orientation of the permanent surface dipole in the supramolecular assembly of the lipid membrane influences the protein attachment to the membrane surface. Analysis of the amide I' mode indicates that the orientation of recoverin bound to the lipid bilayer is independent of the presence of myristoyl chain in the protein and of the folding of the protein into the tense or relaxed state. In contrast, it changes as a function of the membrane potential. At positive transmembrane potentials, the α-helical fragments of recoverin are oriented predominantly parallel to the bilayer surface. This orientation facilitates the insertion of the acyl chain of the protein into the hydrophobic region of the bilayer. At negative transmembrane potentials, the α-helical fragments of recoverin change their orientation with respect to the membrane surface, which is followed by the removal of the myristoyl chain from the membrane.
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Affiliation(s)
| | - Dorota Matyszewska
- Faculty of Chemistry, Biological and Chemical Research Centre , University of Warsaw , ul. Żwirki i Wigury 101 , 02-089 Warsaw , Poland
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6
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Lamb TD, Hunt DM. Evolution of the calcium feedback steps of vertebrate phototransduction. Open Biol 2018; 8:180119. [PMID: 30257895 PMCID: PMC6170504 DOI: 10.1098/rsob.180119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/29/2018] [Indexed: 01/11/2023] Open
Abstract
We examined the genes encoding the proteins that mediate the Ca-feedback regulatory system in vertebrate rod and cone phototransduction. These proteins comprise four families: recoverin/visinin, the guanylyl cyclase activating proteins (GCAPs), the guanylyl cyclases (GCs) and the sodium/calcium-potassium exchangers (NCKXs). We identified a paralogon containing at least 36 phototransduction genes from at least fourteen families, including all four of the families involved in the Ca-feedback loop (recoverin/visinin, GCAPs, GCs and NCKXs). By combining analyses of gene synteny with analyses of the molecular phylogeny for each of these four families of genes for Ca-feedback regulation, we have established the likely pattern of gene duplications and losses underlying the expansion of isoforms, both before and during the two rounds of whole-genome duplication (2R WGD) that occurred in early vertebrate evolution. Furthermore, by combining our results with earlier evidence on the timing of duplication of the visual G-protein receptor kinase genes, we propose that specialization of proto-vertebrate photoreceptor cells for operation at high and low light intensities preceded the emergence of rhodopsin, which occurred during 2R WGD.
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Affiliation(s)
- Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Australian Capital Territory 2600, Australia
| | - David M Hunt
- Centre for Ophthalmology and Visual Science, The Lions Eye Institute, The University of Western Australia, Western Australia 6009, Australia
- School of Biological Sciences, The University of Western Australia, Western Australia 6009, Australia
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7
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Lee TH, Hirst DJ, Kulkarni K, Del Borgo MP, Aguilar MI. Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure. Chem Rev 2018; 118:5392-5487. [PMID: 29793341 DOI: 10.1021/acs.chemrev.7b00729] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Daniel J Hirst
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
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8
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Novel approaches to probe the binding of recoverin to membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:679-691. [DOI: 10.1007/s00249-018-1304-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 02/08/2023]
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9
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Potvin-Fournier K, Lefèvre T, Picard-Lafond A, Marcotte C, Dufresne C, Cantin L, Salesse C, Auger M. Discriminating Lipid– from Protein–Calcium Binding To Understand the Interaction between Recoverin and Phosphatidylglycerol Model Membranes. Biochemistry 2016; 55:3481-91. [DOI: 10.1021/acs.biochem.6b00408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Kim Potvin-Fournier
- Département
de chimie, Regroupement québécois de recherche sur la
fonction, l’ingénierie et les applications des protéines
(PROTEO), Centre de recherche sur les matériaux avancés
(CERMA), Centre québécois sur les matériaux fonctionnels
(CQMF), Université Laval, Pavillon Alexandre-Vachon, 1045
avenue de la médecine, Québec, Québec G1V 0A6, Canada
- CUO-recherche,
Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement,
Département d’ophtalmologie, Faculté de médecine,
PROTEO, Université Laval, Québec, Québec G1S 4L8, Canada
| | - Thierry Lefèvre
- Département
de chimie, Regroupement québécois de recherche sur la
fonction, l’ingénierie et les applications des protéines
(PROTEO), Centre de recherche sur les matériaux avancés
(CERMA), Centre québécois sur les matériaux fonctionnels
(CQMF), Université Laval, Pavillon Alexandre-Vachon, 1045
avenue de la médecine, Québec, Québec G1V 0A6, Canada
| | - Audrey Picard-Lafond
- Département
de chimie, Regroupement québécois de recherche sur la
fonction, l’ingénierie et les applications des protéines
(PROTEO), Centre de recherche sur les matériaux avancés
(CERMA), Centre québécois sur les matériaux fonctionnels
(CQMF), Université Laval, Pavillon Alexandre-Vachon, 1045
avenue de la médecine, Québec, Québec G1V 0A6, Canada
| | - Catherine Marcotte
- Département
de chimie, Regroupement québécois de recherche sur la
fonction, l’ingénierie et les applications des protéines
(PROTEO), Centre de recherche sur les matériaux avancés
(CERMA), Centre québécois sur les matériaux fonctionnels
(CQMF), Université Laval, Pavillon Alexandre-Vachon, 1045
avenue de la médecine, Québec, Québec G1V 0A6, Canada
| | - Caroline Dufresne
- Département
de chimie, Regroupement québécois de recherche sur la
fonction, l’ingénierie et les applications des protéines
(PROTEO), Centre de recherche sur les matériaux avancés
(CERMA), Centre québécois sur les matériaux fonctionnels
(CQMF), Université Laval, Pavillon Alexandre-Vachon, 1045
avenue de la médecine, Québec, Québec G1V 0A6, Canada
| | - Line Cantin
- CUO-recherche,
Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement,
Département d’ophtalmologie, Faculté de médecine,
PROTEO, Université Laval, Québec, Québec G1S 4L8, Canada
| | - Christian Salesse
- CUO-recherche,
Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement,
Département d’ophtalmologie, Faculté de médecine,
PROTEO, Université Laval, Québec, Québec G1S 4L8, Canada
| | - Michèle Auger
- Département
de chimie, Regroupement québécois de recherche sur la
fonction, l’ingénierie et les applications des protéines
(PROTEO), Centre de recherche sur les matériaux avancés
(CERMA), Centre québécois sur les matériaux fonctionnels
(CQMF), Université Laval, Pavillon Alexandre-Vachon, 1045
avenue de la médecine, Québec, Québec G1V 0A6, Canada
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10
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Marino V, Sulmann S, Koch KW, Dell'Orco D. Structural effects of Mg²⁺ on the regulatory states of three neuronal calcium sensors operating in vertebrate phototransduction. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:2055-65. [PMID: 25447547 DOI: 10.1016/j.bbamcr.2014.10.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/25/2014] [Accepted: 10/28/2014] [Indexed: 12/13/2022]
Abstract
The effects of physiological concentration of magnesium on the switch states of the neuronal calcium sensor proteins recoverin, GCAP1 and GCAP2 were investigated. Isothermal titration calorimetry was applied for binding studies. Circular dichroism spectroscopy was used to characterize protein thermal stability, secondary and tertiary structure in conditions of high and low [Ca²⁺], mimicking respectively the dark-adapted and light-exposed photoreceptor states during the phototransduction cascade. Further, molecular dynamics (MD) simulations were run to investigate the dynamical structural properties of GCAP1 in its activator, inhibitor and putative transitory states. Our results confirmed that Mg²⁺ is unable to trigger the typical Ca²⁺-induced conformational change of recoverin (myristoyl switch) while it decreases its thermal stability. Interestingly, Mg²⁺ seems to affect the conformation of GCAP2 both at high and low [Ca²⁺], however the variations are more substantial for myristoylated GCAP2 in the absence of Ca²⁺. GCAP1 is responsive to Mg²⁺ only in its low [Ca²⁺] state and Mg²⁺-GCAP1 tertiary structure slightly differs from both apo and Ca²⁺-bound states. Finally, MD simulations suggest that the GCAP1 state harboring one Mg²⁺ ion bound to EF2 acquires structural characteristics that are thought to be relevant for the activation of the guanylate cyclase. Moreover, all the putative Mg²⁺-bound states of myristoylated GCAP1 are structurally less flexible than Ca²⁺-bound states. GCAP1 acquires a more compact tertiary structure that is less accessible to the solvent, thereby inducing a different conformation to the myristoyl moiety, which might be crucial for the activation of the guanylate cyclase. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.
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Affiliation(s)
- Valerio Marino
- Department of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Italy
| | - Stefan Sulmann
- Department of Neurosciences, Biochemistry Group, University of Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Department of Neurosciences, Biochemistry Group, University of Oldenburg, Germany
| | - Daniele Dell'Orco
- Department of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Italy; Center for BioMedical Computing (CBMC), University of Verona, Italy.
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11
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Ca 2 + and Mg 2 + binding induce conformational stability of Calfumirin-1 from Dictyostelium discoideum. J CHEM SCI 2014. [DOI: 10.1007/s12039-014-0615-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Kahlen J, Salimi L, Sulpizi M, Peter C, Donadio D. Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields. J Phys Chem B 2014; 118:3960-72. [DOI: 10.1021/jp412490c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Kahlen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Leila Salimi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Christine Peter
- University of Konstanz, P.O. Box 718, 78547 Konstanz, Germany
| | - Davide Donadio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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13
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Potvin-Fournier K, Lefèvre T, Picard-Lafond A, Valois-Paillard G, Cantin L, Salesse C, Auger M. The thermal stability of recoverin depends on calcium binding and its myristoyl moiety as revealed by infrared spectroscopy. Biochemistry 2013; 53:48-56. [PMID: 24359287 DOI: 10.1021/bi401336g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To evaluate the structural stability of recoverin, a member of the neuronal calcium sensor family, the effect of temperature, myristoylation, and calcium:protein molar ratio on its secondary structure has been studied by transmission infrared spectroscopy. On the basis of the data, the protein predominantly adopts α-helical structures (∼50-55%) with turns, unordered structures, and β-sheets at 25 °C. The data show no significant impact of the presence of calcium and myristoylation on secondary structure. It is found that, in the absence of calcium, recoverin denatures and self-aggregates while being heated, with the formation of intermolecular antiparallel β-sheets. The nonmyristoylated protein (Rec-nMyr) exhibits a lower temperature threshold of aggregation and a higher intermolecular β-sheet content at 65 °C than the myristoylated protein (Rec-Myr). The former thus appears to be less thermally stable than the latter. In the presence of excess calcium ions (calcium:protein ratio of 10), the protein is thermally stable up to 65 °C with no significant conformational change, the presence of the myristoyl chain having no effect on the thermal stability of recoverin under these conditions. A decrease in the thermal stability of recoverin is observed as the calcium:protein molar ratio decreases, with Rec-nMyr being less stable than Rec-Myr. The data overall suggest that a minimal number of coordinated calcium ions is necessary to fully stabilize the structure of recoverin and that, when bound to the membrane, i.e., when the myristoyl chain protrudes from the interior pocket, recoverin should be more stable than in a Ca-free solution, i.e., when the myristoyl chain is sequestered in the interior.
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Affiliation(s)
- Kim Potvin-Fournier
- Département de chimie, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Université Laval , Pavillon Alexandre-Vachon, 1045 avenue de la médecine, Québec, Québec G1V 0A6, Canada
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Suzuki N, Imai LF, Kato Y, Nagata K, Ohashi Y, Kuchitsu K, Tanokura M, Sakamoto A, Nara M, Nakano M, Yonezawa N. Coordination structures of Mg2+ and Ca2+ in three types of tobacco calmodulins in solution: Fourier-transform infrared spectroscopic studies of side-chain COO- groups. Biopolymers 2013; 99:472-83. [PMID: 23616215 DOI: 10.1002/bip.22203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/25/2012] [Accepted: 01/05/2013] [Indexed: 12/16/2023]
Abstract
Calmodulin (CaM) is a Ca(2+)-binding protein that regulates a number of fundamental cellular activities. Nicotiana tabacum CaM (NtCaM) comprises 13 genes classified into three types, among which gene expression and target enzyme activation differ. We performed Fourier-transform infrared spectroscopy to compare the secondary and coordination structures of Mg(2+) and Ca(2+) among NtCaM1, NtCaM3, and NtCaM13 as representatives of the three types of NtCaMs. Data suggested that NtCaM13 has a different secondary structure due to the weak β-strand bands and the weak 1661 cm(-1) band. Coordination structures of Mg(2+) of NtCaM3 and NtCaM13 were similar but different from that of NtCaM1, while the Ca(2+)-binding manner was similar among the three CaMs. The amplitude differences of the band at 1554-1550 cm(-1) obtained by second-derivative spectra indicated that the intensity change of the band of NtCaM13 was smaller in response to [Ca(2+)] increases under low [Ca(2+)] conditions than were those of NtCaM1 and NtCaM3, while the intensity reached the same level under high [Ca(2+)]. Therefore, NtCaM13 has a characteristic secondary structure and specific Mg(2+)-binding manner and needs higher [Ca(2+)] for bidentate Ca(2+) coordination of 12th Glu in EF-hand motifs. The Ca(2+)-binding mechanisms of the EF-hand motifs of the three CaMs are similar; however, the cation-dependent conformational change in NtCaM13 is unique among the three NtCaMs.
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Affiliation(s)
- Nanao Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
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15
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Nara M, Morii H, Tanokura M. Coordination to divalent cations by calcium-binding proteins studied by FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012. [PMID: 23201542 DOI: 10.1016/j.bbamem.2012.11.025] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We review the Fourier-transform infrared (FTIR) spectroscopy of side-chain COO(-) groups of Ca(2+)-binding proteins: parvalbumins, bovine calmodulin, akazara scallop troponin C and related calcium binding proteins and peptide analogues. The COO(-) stretching vibration modes can be used to identify the coordination modes of COO(-) groups of Ca(2+)-binding proteins to metal ions: bidentate, unidentate, and pseudo-bridging. FTIR spectroscopy demonstrates that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site in solution. The interpretation of COO(-) stretches is ensured on the basis of the spectra of calcium-binding peptide analogues. The implication of COO(-) stretches is discussed for Ca(2+)-binding proteins. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Masayuki Nara
- Laboratory of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Chiba 272-0827, Japan.
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16
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Biophysical investigation of retinal calcium sensor function. Biochim Biophys Acta Gen Subj 2011; 1820:1228-33. [PMID: 22020050 DOI: 10.1016/j.bbagen.2011.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/05/2011] [Accepted: 10/06/2011] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neuronal calcium sensor proteins represent a subgroup of the family of EF-hand calcium binding proteins. Members of this subgroup are the guanylate cyclase-activating proteins and recoverin, which operate as important calcium sensors in retinal photoreceptor cells. Physiological and biochemical data indicate that these proteins participate in shaping the photoreceptor light response. SCOPE OF REVIEW Biophysical methods have been widely applied to investigate the molecular properties of retinal calcium binding proteins like the guanylate cyclase-activating proteins and recoverin. Properties include the determination of calcium affinities by isotope techniques and spectroscopical approaches. Conformational changes are investigated for example by tryptophan fluorescence emission. A special focus of this review is laid on a new experimental approach to study conformational changes in calcium binding proteins by surface plasmon resonance spectroscopy. In addition this technique has been employed for measuring the calcium-dependent binding of calcium sensors to membranes. MAJOR CONCLUSIONS Biophysical approaches provide valuable information about key properties of calcium sensor proteins involved in intracellular signalling. Parameters of their molecular properties like calcium binding and conformational changes help to define their physiological role derived from cellular, genetic or physiological studies. GENERAL SIGNIFICANCE Calcium is an important second messenger in intracellular signaling. Calcium signals are propagated via calcium binding proteins that are able to discriminate between incremental differences in intracellular calcium and that regulate their targets with high precision and specificity. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signalling.
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17
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Nullmeier M, Koliwer-Brandl H, Kelm S, Zägel P, Koch KW, Brand I. Impact of Strong and Weak Lipid-Protein Interactions on the Structure of a Lipid Bilayer on a Gold Electrode Surface. Chemphyschem 2011; 12:1066-79. [DOI: 10.1002/cphc.201100036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 02/07/2011] [Indexed: 01/13/2023]
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18
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Appoh FE, Kraatz HB. Voltammetric studies of dendrimer multilayers: Layer-by-layer assembly of metal-peptide dendrimers multilayers. J Appl Polym Sci 2009. [DOI: 10.1002/app.28980] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Abstract
Oxidation of methionine residues in calmodulin (CaM) lowers the affinity for calcium and results in an inability to activate target proteins fully. To evaluate the structural consequences of CaM oxidation, we used infrared difference spectroscopy to identify oxidation-dependent effects on protein conformation and calcium liganding. Oxidation-induced changes include an increase in hydration of alpha-helices, as indicated in the downshift of the amide I' band of both apo-CaM and Ca(2+)-CaM, and a modification of calcium liganding by carboxylate side chains, reflected in antisymmetric carboxylate band shifts. Changes in carboxylate ligands are consistent with the model we propose: an Asp at position 1 of the EF-loop experiences diminished hydrogen bonding with the polypeptide backbone, an Asp at position 3 forms a bidentate coordination of calcium, and an Asp at position 5 forms a pseudobridging coordination with a calcium-bound water molecule. The bidentate coordination of calcium by conserved glutamates is unaffected by oxidation. The observed changes in calcium ligation are discussed in terms of the placement of methionine side chains relative to the calcium-binding sites, suggesting that varying sensitivities of binding sites to oxidation may underlie the loss of CaM function upon oxidation.
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20
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Aravind P, Chandra K, Reddy PP, Jeromin A, Chary K, Sharma Y. Regulatory and Structural EF-Hand Motifs of Neuronal Calcium Sensor-1: Mg2+ Modulates Ca2+ Binding, Ca2+-Induced Conformational Changes, and Equilibrium Unfolding Transitions. J Mol Biol 2008; 376:1100-15. [DOI: 10.1016/j.jmb.2007.12.033] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2007] [Revised: 12/11/2007] [Accepted: 12/17/2007] [Indexed: 11/26/2022]
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21
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Nara M, Tanokura M. Infrared spectroscopic study of the metal-coordination structures of calcium-binding proteins. Biochem Biophys Res Commun 2008; 369:225-39. [PMID: 18182161 DOI: 10.1016/j.bbrc.2007.11.188] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 11/15/2007] [Indexed: 11/30/2022]
Abstract
Carboxylate (COO(-)) groups can coordinate to metal ions in of the following four modes: 'unidentate', 'bidentate', 'bridging' and 'pseudo-bridging' modes. COO(-) stretching frequencies provide information about the coordination modes of COO(-) groups to metal ions. We review the Fourier-transform infrared spectroscopy (FTIR) of side-chain COO(-) groups of Ca(2+)-binding proteins: pike parvalbumin pI 4.10, bovine calmodulin and Akazara scallop troponin C. FTIR spectroscopy of Akazara scallop troponin C has demonstrated that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site. The assignments of the COO(-) antisymmetric stretch have been ensured on the basis of the spectra of calcium-binding peptide analogues. The downshift of the COO(-) antisymmetric stretching mode from 1565 cm(-1) to 1555-1540 cm(-1) upon Ca(2+) binding is a commonly observed feature of FTIR spectra for EF-hand proteins.
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Affiliation(s)
- Masayuki Nara
- Laboratory of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Chiba 272-0827, Japan
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22
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Desmeules P, Penney SE, Desbat B, Salesse C. Determination of the contribution of the myristoyl group and hydrophobic amino acids of recoverin on its dynamics of binding to lipid monolayers. Biophys J 2007; 93:2069-82. [PMID: 17526567 PMCID: PMC1959526 DOI: 10.1529/biophysj.106.103481] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 05/17/2007] [Indexed: 01/16/2023] Open
Abstract
It has been postulated that myristoylation of peripheral proteins would facilitate their binding to membranes. However, the exact involvement of this lipid modification in membrane binding is still a matter of debate. Proteins containing a Ca(2+)-myristoyl switch where the extrusion of their myristoyl group is dependent on calcium binding is best illustrated by the Ca(2+)-binding recoverin, which is present in retinal rod cells. The parameters responsible for the modulation of the membrane binding of recoverin are still largely unknown. This study was thus performed to determine the involvement of different parameters on recoverin membrane binding. We have used surface pressure measurements and PM-IRRAS spectroscopy to monitor the adsorption of myristoylated and nonmyristoylated recoverin onto phospholipid monolayers in the presence and absence of calcium. The adsorption curves have shown that the myristoyl group and hydrophobic residues of myristoylated recoverin strongly accelerate membrane binding in the presence of calcium. In the case of nonmyristoylated recoverin in the presence of calcium, hydrophobic residues alone are responsible for its much faster monolayer binding than myristoylated and nonmyristoylated recoverin in the absence of calcium. The infrared spectra revealed that myristoylated and nonmyristoylated recoverin behave very different upon adsorption onto phospholipid monolayers. Indeed, PM-IRRAS spectra indicated that the myristoyl group allows a proper orientation and organization as well as faster and stronger binding of myristoylated recoverin to lipid monolayers compared to nonmyristoylated recoverin. Simulations of the spectra have allowed us to postulate that nonmyristoylated recoverin changes conformation and becomes hydrated at large extents of adsorption as well as to estimate the orientation of myristoylated recoverin with respect to the monolayer plane. In addition, adsorption measurements and electrophoresis of trypsin-treated myristoylated recoverin in the presence of zinc or calcium demonstrated that recoverin has a different conformation but a similar extent of monolayer binding in the presence of such ions.
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Affiliation(s)
- Philippe Desmeules
- Unité de Recherche en Opthalmologie, Centre Hospitalier Universitaire de Québec, Pavillon CHUL, and Département d'Opthalmologie, Faculté de Médecine, Université Laval, Québec, Canada
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23
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Dudev T, Lim C. Effect of carboxylate-binding mode on metal binding/selectivity and function in proteins. Acc Chem Res 2007; 40:85-93. [PMID: 17226948 DOI: 10.1021/ar068181i] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We delineate the factors governing the carboxylate-binding mode (monodentate vs bidentate) in metalloproteins. We reveal how the carboxylate-binding mode affects the binding affinity and selectivity of a metal ion as well as the function of a metalloprotein using Ca2+-binding proteins and enzymes (ribonuclease H1, phosphoserine phosphatase, and ribonucleotide reductase) as examples. The collected data indicate that a carboxylate monodentate left arrow over right arrow bidentate switch, in addition to other structural factors, could be used to fine tune the metal-binding site affinity and/or selectivity, thus modifying the function/properties of the metalloprotein.
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Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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24
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Jheng FF, Wang L, Lee L, Chang LS. Functional Contribution of Ca2+ and Mg2+ to the Intermolecular Interaction of Visinin-like Proteins. Protein J 2006; 25:250-6. [PMID: 16703469 DOI: 10.1007/s10930-006-9008-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The interaction of human visinin-like protein 1 (VILIP1) and visinin-like protein 3 (VILIP3) with divalent cations (Mg2+, Ca2+, Sr2+ and Ba2+) was explored using circular dichroism and fluorescence measurement. These results showed that the four cations each induced a different subtle change in the conformation of VILIPs. Moreover, VILIP1 and VILIP3 bound with Ca2+ or Mg2+ in a cooperative manner. Studies on the truncated mutants showed that the intact EF-3 and EF-4 were essential for the binding of VILIP1 with Ca2+ and Mg2+. Pull-down assay revealed that Ca2+ and Mg2+ enhanced the intermolecular interaction of VILIPs, and led to the formation of homo- and hetero-oligomer of VILIPs. Together with previous findings that Ca2+-dependent localization of VILIPs may be involved in the regulation of distinct cascades and deprivation of Ca2+-binding capacity of VILIPs did not completely eliminate their activity, it is likely to reflect that Mg2+-bound VILIPs may play a role in regulating the biological function of VILIPs in response to a concentration fluctuation of Ca2+ in cells.
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Affiliation(s)
- Feng-Fin Jheng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
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25
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Dudev T, Chang LY, Lim C. Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study. J Am Chem Soc 2005; 127:4091-103. [PMID: 15771547 DOI: 10.1021/ja044404t] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trivalent lanthanide cations are extensively being used in biochemical experiments to probe various dication-binding sites in proteins; however, the factors governing the binding specificity of lanthanide cations for these binding sites remain unclear. Hence, we have performed systematic studies to evaluate the interactions between La3+ and model Ca2+ - and Mg2+ -binding sites using density functional theory combined with continuum dielectric methods. The calculations reveal the key factors and corresponding physical bases favoring the substitution of trivalent lanthanides for divalent Ca2+ and Mg2+ in holoproteins. Replacing Ca2+ or Mg2+ with La3+ is facilitated by (1) minimizing the solvent exposure and the flexibility of the metal-binding cavity, (2) freeing both carboxylate oxygen atoms of Asp/Glu side chains in the metal-binding site so that they could bind bidentately to La3+, (3) maximizing the number of metal-bound carboxylate groups in buried sites, but minimizing the number of metal-bound carboxylate groups in solvent-exposed sites, and (4) including an Asn/Gln side chain for sites lined with four Asp/Glu side chains. In proteins bound to both Mg2+ and Ca2+, La3+ would prefer to replace Ca2+, as compared to Mg2+. A second Mg2+-binding site with a net positive charge would hamper the Mg2+ --> La3+ exchange, as compared to the respective mononuclear site, although the La3+ substitution of the first native metal is more favorable than the second one. The findings of this work are in accord with available experimental data.
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Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
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26
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Appoh FE, Sutherland TC, Kraatz HB. Ferrocenoyl-amino acids: redox response towards di- and trivalent metal ions. J Organomet Chem 2005. [DOI: 10.1016/j.jorganchem.2004.11.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Rollin-Genetet F, Berthomieu C, Davin AH, Quéméneur E. Escherichia coli thioredoxin inhibition by cadmium: two mutually exclusive binding sites involving Cys32 and Asp26. ACTA ACUST UNITED AC 2004; 271:1299-309. [PMID: 15030480 DOI: 10.1111/j.1432-1033.2004.04037.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Observations of thioredoxin inhibition by cadmium and of a positive role for thioredoxin in protection from Cd(2+) led us to investigate the thioredoxin-cadmium interaction properties. We used calorimetric and spectroscopic methods at different pH values to explore the relative contribution of putative binding residues (Cys32, Cys35, Trp28, Trp31 and Asp26) within or near the active site. At pH 8 or 7.5 two binding sites were identified by isothermal titration calorimetry with affinity constants of 10 x 10(6) m(-1) and 1 x 10(6) m(-1). For both sites, a proton was released upon Cd(2+) binding. One mole of Cd(2+) per mole of reduced thioredoxin was measured by mass spectrometry at these pH values, demonstrating that the two binding sites were partially occupied and mutually exclusive. Cd(2+) binding at either site totally inhibited the thiol-disulfide transferase activity of Trx. The absence of Cd(2+) interaction detected for oxidized or alkylated Trx and the inhibition of the enzymatic activity of thioredoxin by Cd(2+) supported the role of Cys32 at the first site. The fluorescence profile of Cd(2+)-bound thioredoxin differed, however, from that of oxidized thioredoxin, indicating that Cd(2+) was not coordinated with Cys32 and Cys35. From FTIR spectroscopy, we inferred that the second site might involve Asp26, a buried residue that deprotonates at a rather high and unusual pK(a) for a carboxylate (7.5/9.2). The pK(a) of the two residues Cys32 and Asp26 have been shown to be interdependent [Chivers, T. P. (1997) Biochemistry36, 14985-14991]. A mechanism is proposed in which Cd(2+) binding at the solvent-accessible thiolate group of Cys32 induces a decrease of the pK(a) of Asp26 and its deprotonation. Conversely, interaction between the carboxylate group of Asp26 and Cd(2+) at a second binding site induces Cys32 deprotonation and thioredoxin inhibition, so that Cd(2+) inhibits thioredoxin activity not only by binding at the Cys32 but also by interacting with Asp26.
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Affiliation(s)
- Françoise Rollin-Genetet
- CEA Valrhô, DSV-DIEP, Service de Biochimie postgénomique et Toxicologie Nucléaire, Bagnols-sur-Cèze, France.
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28
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Dudev T, Lim C. Monodentate versus Bidentate Carboxylate Binding in Magnesium and Calcium Proteins: What Are the Basic Principles? J Phys Chem B 2004. [DOI: 10.1021/jp0310347] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, Republic of China, and Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan, Republic of China
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, Republic of China, and Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan, Republic of China
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Peshenko IV, Dizhoor AM. Guanylyl cyclase-activating proteins (GCAPs) are Ca2+/Mg2+ sensors: implications for photoreceptor guanylyl cyclase (RetGC) regulation in mammalian photoreceptors. J Biol Chem 2004; 279:16903-6. [PMID: 14993224 DOI: 10.1074/jbc.c400065200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Guanylyl cyclase-activating proteins (GCAP) are EF-hand Ca(2+)-binding proteins that activate photoreceptor guanylyl cyclase (RetGC) in the absence of Ca(2+) and inhibit RetGC in a Ca(2+)-sensitive manner. The reported data for the RetGC inhibition by Ca(2+)/GCAPs in vitro are in disagreement with the free Ca(2+) levels found in mammalian photoreceptors (Woodruff, M. L., Sampath, A. P., Matthews, H. R., Krasnoperova, N. V., Lem, J., and Fain, G. L. (2002) J. Physiol. (Lond.) 542, 843-854). We have found that binding of Mg(2+) dramatically affects both Ca(2+)-dependent conformational changes in GCAP-1 and Ca(2+) sensitivity of RetGC regulation by GCAP-1 and GCAP-2. Lowering free Mg(2+) concentrations ([Mg](f)) from 5.0 mm to 0.5 mm decreases the free Ca(2+) concentration required for half-maximal inhibition of RetGC ([Ca]((1/2))) by recombinant GCAP-1 and GCAP-2 from 1.3 and 0.2 microm to 0.16 and 0.03 microm, respectively. A similar effect of Mg(2+) on Ca(2+) sensitivity of RetGC by endogenous GCAPs was observed in mouse retina. Analysis of the [Ca]((1/2)) changes as a function of [Mg](f) in mouse retina shows that the [Ca]((1/2)) becomes consistent with the range of 23-250 nm free Ca(2+) found in mouse photoreceptors only if the [Mg](f) in the photoreceptors is near 1 mm. Our data demonstrate that GCAPs are Ca(2+)/Mg(2+) sensor proteins. While Ca(2+) binding is essential for cyclase activation and inhibition, Mg(2+) binding to GCAPs is critical for setting the actual dynamic range of RetGC regulation by GCAPs at physiological levels of free Ca(2+).
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Affiliation(s)
- Igor V Peshenko
- Hafter Research Laboratory, Pennsylvania College of Optometry, Elkins Park, Pennsylvania 19027
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30
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Novel determination of cadmium ions using an enzyme self-assembled monolayer with surface plasmon resonance. Anal Chim Acta 2003. [DOI: 10.1016/s0003-2670(03)00943-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Dudev T, Lin YL, Dudev M, Lim C. First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations. J Am Chem Soc 2003; 125:3168-80. [PMID: 12617685 DOI: 10.1021/ja0209722] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.
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Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan ROC
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32
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Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.
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Mozsolits H, Thomas WG, Aguilar MI. Surface plasmon resonance spectroscopy in the study of membrane-mediated cell signalling. J Pept Sci 2003; 9:77-89. [PMID: 12630693 DOI: 10.1002/psc.439] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Peptide-membrane interactions contribute to many important biological processes such as cellular signaling, protein trafficking and ion-channel formation. During receptor-mediated signalling, activated intracellular signalling molecules are often recruited into receptor-induced signaling complexes at the cytoplasmic surface of the cell membrane. Such recruitment can depend upon protein-protein and protein-lipid interactions as well as protein acylation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study these interactions and have provided important information on the relationship between the structure of these proteins involved in cell signalling and their biological function. More recently, surface plasmon resonance (SPR) spectroscopy has also been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications, which demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated cellular signalling.
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Affiliation(s)
- Henriette Mozsolits
- Department of Biochemistry and Molecular Biology, PO Box 13D, Monash University, Clayton 3800, Victoria, Australia
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IMURA T, YANAGISHITA H, IKEGAMI T, NEGISHI H, KITAMOTO D. Drastic Improvements in Trapping Efficiency and Dispersibility for Phosphatidylcholine Liposomes in the Presence of Divalent Metal Ions. J Oleo Sci 2003. [DOI: 10.5650/jos.52.673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Paynter S, Russell DA. Surface plasmon resonance measurement of pH-induced responses of immobilized biomolecules: conformational change or electrostatic interaction effects? Anal Biochem 2002; 309:85-95. [PMID: 12381366 DOI: 10.1016/s0003-2697(02)00255-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recently, the observation of pH-induced conformational changes of biomolecules supported on carboxymethyldextran (CMD)-coated surfaces measured using surface plasmon resonance (SPR) has been reported. However, it is apparent that the evidence reported in the literature is ambiguous. The research presented in this paper describes investigations to study the changing SPR signal of immobilized biomolecules as a function of varying pH, to provide a detailed understanding of the origin of the pH-induced changes in the SPR profile. SPR measurements were performed with cytochrome c, concanavalin A, and poly-L-lysine, biomolecules that exhibit diverse conformational responses to changing pH, covalently immobilized onto CMD-coated supports. These SPR measurements were supported by circular dichroism (CD) solution studies. The SPR profiles recorded were not consistent with the conformational transitions of the biomolecules as observed using CD. An alternative explanation for the observed shifts in SPR is proposed, which explains the SPR profiles in terms of electrostatic interaction effects between the immobilized biomolecules and the carboxymethyldextran matrix.
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Affiliation(s)
- Sally Paynter
- School of Chemical Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK
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Umezawa Y, Ozawa T, Sato M. Probing Chemical Processes in Living Cells: Applications for Assay and Screening of Chemicals that Disrupt Cellular Signaling Pathways. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.1423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Umezawa Y, Ozawa T, Sato M. Methods of analysis for chemicals that promote/disrupt cellular signaling. ANAL SCI 2002; 18:503-16. [PMID: 12036116 DOI: 10.2116/analsci.18.503] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Methods of analysis were presented for chemicals that promote or disrupt cellular signaling pathways. The developed analytical methods are based not only on receptor binding, but also on the following known molecular-level processes involved in signal transduction along signaling pathways, reconstituted in vitro or taken in part in living cells. The methods were discussed in relation to receptor binding assay and/or bioassay. Examples include: (1) Insulin signaling pathways; (1-i) Chemical selectivity of agonists for insulin signaling pathways based on agonist-induced phosphorylation of a target peptide; (1-ii) An SPR-based screening method for agonist selectivity for insulin signaling pathways based on the binding of phosphotyrosine to its specific binding protein; (1-iii) A fluorescent indicator for tyrosine phosphorylation-based insulin signaling pathways; (2) An optical method for evaluating ion selectivity for calcium signaling pathways in the cell; (3) Assay and screening of chemicals that disrupt cellular signaling pathways, potential endocrine disruptors in particular; (4) Protein conformational changes, and (5) A screening method for antigen-specific IgE using mast cells, based on intracellular calcium signaling.
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Affiliation(s)
- Yoshio Umezawa
- Department of Chemistry, School of Science, The University of Tokyo, Bunkyo, Japan.
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Yumoto F, Nara M, Kagi H, Iwasaki W, Ojima T, Nishita K, Nagata K, Tanokura M. Coordination structures of Ca2+ and Mg2+ in Akazara scallop troponin C in solution. FTIR spectroscopy of side-chain COO- groups. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:6284-90. [PMID: 11733025 DOI: 10.1046/j.1432-1327.2001.02583.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
FTIR spectroscopy has been applied to study the coordination structures of Mg2+ and Ca2+ ions bound in Akazara scallop troponin C (TnC), which contains only a single Ca2+ binding site. The region of the COO- antisymmetric stretch provides information about the coordination modes of COO- groups to the metal ions: bidentate, unidentate, or pseudo-bridging. Two bands were observed at 1584 and 1567 cm-1 in the apo state, whereas additional bands were observed at 1543 and 1601 cm-1 in the Ca2+-bound and Mg2+-bound states, respectively. The intensity of the band at 1567 cm-1 in the Mg2+-bound state was identical to that in the apo state. Therefore, the side-chain COO- group of Glu142 at the 12th position in the Ca2+-binding site coordinates to Ca2+ in the bidentate mode but does not interact with Mg2+ directly. A slight upshift of COO- antisymmetric stretch due to Asp side-chains was also observed upon Mg2+ and Ca2+ binding. This indicates that the COO- groups of Asp131 and Asp133 interact with both Ca2+ and Mg2+ in the pseudo-bridging mode. Therefore, the present study directly demonstrated that the coordination structure of Mg2+ was different from that of Ca2+ in the Ca2+-binding site. In contrast to vertebrate TnC, most of the secondary structures remained unchanged among apo, Mg2+-bound and Ca2+-bound states of Akazara scallop TnC, as spectral changes upon either Ca2+ or Mg2+ binding were very small in the infrared amide-I' region as well as in the CD spectra. Fluorescence spectroscopy indicated that the spectral changes upon Ca2+ binding were larger than that upon Mg2+ binding. Moreover, gel-filtration experiments indicated that the molecular sizes of TnC had the order apo TnC > Mg2+-bound TnC > Ca2+-bound TnC. These results suggest that the tertiary structures are different in the Ca2+- and Mg2+-bound states. The present study may provide direct evidence that the side-chain COO- groups in the Ca2+-binding site are directly involved in the functional on/off mechanism of the activation of Akazara scallop TnC.
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Affiliation(s)
- F Yumoto
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
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Affiliation(s)
- W Cho
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, USA.
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Abstract
We have compiled a comprehensive list of the articles published in the year 2000 that describe work employing commercial optical biosensors. Selected reviews of interest for the general biosensor user are highlighted. Emerging applications in areas of drug discovery, clinical support, food and environment monitoring, and cell membrane biology are emphasized. In addition, the experimental design and data processing steps necessary to achieve high-quality biosensor data are described and examples of well-performed kinetic analysis are provided.
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Affiliation(s)
- R L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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